The aberration-corrected STEM allows nanostructures to be investigated with greater resolution and sensitivity than ever before. Single atom sensitivity is achieved both in imaging and also for spectroscopy, for atoms on surfaces or within the bulk. Nanocrystal size, shape, surface termination, 3D structure and the presence of any defects can be seen with unprecedented ease. The improved sensitivity provides improved input for theory, allowing new insights into nanostructure properties and the origin of their unique functionality. Furthermore, the larger aperture available with aberration-corrected STEM improves the depth resolution dramatically. Nanometer depth resolution can be achieved by simply taking a focal series of images, which may then be reconstructed into a 3D rendering of the material in the same manner as with confocal optical microscopy but maintaining sensitivity to individual atoms.